grinch | global report investigating novel coronavirus haplotypes

New variant report 2020-12-31

Data source and processing

This report is recent as of 2020-12-31 14:02 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.4, pangoLEARN version 2020-12-17-2.

Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs – defined here – and B.1.351 to any sequences with more than 3 of the 5 defining B.1.351 SNPs.

Table 1 | Summary of data

Lineage	Country count	Country	Sequence count	Earliest sequence	Travel history
B.1.351	4	South_Africa 322, Switzerland 2, Finland 1, UK 1	326	2020-10-08
B.1.1.7	21	UK 4518, Denmark 33, Portugal 20, Italy 17, Netherlands 8, Ireland 7, Australia 4, Israel 4, South_Korea 3, India 3, Finland 2, Norway 2, USA 2, Hong_Kong 2, Spain 1, Sweden 1, Canada 1, Switzerland 1, Germany 1, Singapore 1, France 1	4632	2020-09-20

Lineage B.1.351

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.351 | Lineage B.1.351

Statistic	Information
Count	326
Likely origin	South Africa
SNPs	aa:orf1ab:K1655N aa:S:D215G aa:S:E484K aa:S:N501Y snp:C23664T

Figure 1 | Cumulative sequence count over time B.1.351

Figure 2 | Date of earliest B.1.351 detected

Figure 3 | Map of B.1.351 sequence counts

Figure 4 | Sequence count per country B.1.351

Figure 5 | Frequency B.1.351 in sequences produced since first new variant reported per country

Figure 6 | B.1.351 count per country

Figure 7 | Rolling average B.1.351 frequency per country

Lineage B.1.1.7

Table B.1.1.7 | Lineage B.1.1.7

Statistic	Information
Count	4632
Likely origin	United Kingdom
SNPs	aa:orf1ab:T1001I aa:orf1ab:A1708D aa:orf1ab:I2230T del:11288:9 del:21765:6 del:21991:3 aa:S:N501Y aa:S:A570D aa:S:P681H aa:S:T716I aa:S:S982A aa:S:D1118H aa:Orf8:Q27* aa:Orf8:R52I aa:Orf8:Y73C aa:N:D3L aa:N:S235F

Figure 8 | Cumulative sequence count over time B.1.1.7

Figure 9 | Date of earliest B.1.1.7 detected

Figure 10 | Map of B.1.1.7 sequence counts

Figure 11 | Sequence count per country B.1.1.7

Figure 12 | Frequency B.1.1.7 in sequences produced since first new variant reported per country

Figure 13 | B.1.1.7 count per country

Figure 14 | Rolling average B.1.1.7 frequency per country

Figure 11 | Air traffic from UK by destination

The number of ticketed origin-to-destination journeys from London airports to countries outside the United Kingdom during October 2020.

Colours indicate numbers of published genomes of B.1.1.7 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.1.7 sequences on GISAID. White bars indicate countries with no reports of B.1.1.7.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.

Data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer